Oops, thanks for pointing this out!
We have just updated the wiki and website with info of the release now.
Best
// Samuel
On 2016-11-04 10:07, Peter Maas wrote:
>
> Interesting but I can’t find any documentation on this update
>
> Blogs, IRC channels, wiki, home pages and everything else seems
> several years old.
>
> Even in the source files in sourceforge and git commits seem 3 years old.
>
> But I was able to install and run it.
>
> Thanks,
>
> Peter
>

On Fri, Nov 4, 2016 at 10:07 AM, Peter Maas <peter.maas@...> wrote:
> Interesting but I can’t find any documentation on this update
>
> Blogs, IRC channels, wiki, home pages and everything else seems several
> years old.
Hm yea I think blogging activity is down for the moment and I think we
have drifted away from IRC as main communicational channel although
most of us still hang out there in case someone has questions.
Personally I must admit that I haven't done much actual Bioclipse
coding in years though.
> Even in the source files in sourceforge and git commits seem 3 years old.
Yea development no longer takes place on sourceforge. The repositories
has moved to Github (https://github.com/bioclipse)
--
// Jonathan

Interesting but I can’t find any documentation on this update
Blogs, IRC channels, wiki, home pages and everything else seems several years old.
Even in the source files in sourceforge and git commits seem 3 years old.
But I was able to install and run it.
Thanks,
Peter
From: Arvid Berg [mailto:goglepox@...]
Sent: Thursday, November 03, 2016 6:59 PM
To: bioclipse-users@...; Bioclipse-devel ML
Subject: [Bioclipse-devel] Bioclipse 2.6.2 released
Bioclipse 2.6.2 is now releases and available for download from <https://sourceforge.net/projects/bioclipse/&gt; sourceforge.net
This release contains bugfixes and compatibility improvements.
// The Bioclipse team

Hi Nick,
There is a change in how Windows 10 reports its version to java that is
causing troubles in Bioclipse.
We have implemented a workaround in our upcoming release, if you go to
http://wiki.bioclipse.net/index.php?title=Download you can download
Bioclipse "2.6.2 (beta)" for your platform.
To be able to install the latest features you need to go to
'Preferences...->Install/Update->Available Software Sites' and change
http://update.bioclipse.net to http://devel.bioclipse.net
Regards,
Arvid
2016-01-06 20:31 GMT+01:00 Nick Price <nick@...>:
> Hi,
> I have recently upgraded to Windows 10 via the Microsoft upgrade system
> (not a clean re-install).
> I was previously using Windows 7 with Bioclipse running the Decision
> support, QSAR, and Opentox extensions.
> My "in place" Bioclipse installation refused to acknowledge the presence
> of the extensions once windows 10 was running, so I removed Bioclipse,
> downloaded the zip file afresh, and started again. Bioslipse installed
> fine, and all the extensions and added features installed fine too.
> However when Bioclipse was run, none of these extensions were available.
> According to Bioclipse, all the extensions were installed but none is
> available to use.
> I'm sure there's other information you need before you can suggest
> what's causing my problems ?
>
> Regards,
> Nick
>
> --
> Professor N.R.Price. B.A, PhD
> Technology for Growth
> Oak Lea
> Marton
> Sinnington
> York YO62 6RD
> UK
> http://www.technologyforgrowth.co.uk
>
> "Science and everyday life cannot, and should not be separated" Rosalind
> Franklin
>
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Bioclipse-users mailing list
> Bioclipse-users@...
> https://lists.sourceforge.net/lists/listinfo/bioclipse-users
>

Hi,
I have recently upgraded to Windows 10 via the Microsoft upgrade system
(not a clean re-install).
I was previously using Windows 7 with Bioclipse running the Decision
support, QSAR, and Opentox extensions.
My "in place" Bioclipse installation refused to acknowledge the presence
of the extensions once windows 10 was running, so I removed Bioclipse,
downloaded the zip file afresh, and started again. Bioslipse installed
fine, and all the extensions and added features installed fine too.
However when Bioclipse was run, none of these extensions were available.
According to Bioclipse, all the extensions were installed but none is
available to use.
I'm sure there's other information you need before you can suggest
what's causing my problems ?
Regards,
Nick
--
Professor N.R.Price. B.A, PhD
Technology for Growth
Oak Lea
Marton
Sinnington
York YO62 6RD
UK
http://www.technologyforgrowth.co.uk
"Science and everyday life cannot, and should not be separated" Rosalind Franklin

Hi all,
Jena3 has been released and is the way forward. The API has changed a
bit, but the core functionality is equivalent and I managed to upgrade
this.
However, not all current plugins will survive the upgrade. In
particular, Pellet will not make the update (along with the OWL manger
which used that; use the OWLAPI manager instead), as the current
library is no longer open source, and I would have to update the open
source version myself (I have no intention too). The new LDF feature
may also be temporary be offline, but the authors of that were happy
with HDT upgrading, and I expect them to follow soon, so that I can
update that too.
So, my question to everyone is: is someone depending on Jena2.x in
Bioclipse? This would be a good time to let me know. At a rdf manager
level nothing will change.
Looking forward to hearing from you,
greetings,
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen

There is a thread specific container (singleton I think) for the scripting
monitors, i.e., the monitor used when running BSL. Don't remember the name
of it but I think you just call it with the correct thread and you get the
proper monitor.
(maybe we should move over to the develop list instead? egonw are you on
that?)
On Sun, Jul 26, 2015 at 11:24 AM, Egon Willighagen <
egon.willighagen@...> wrote:
> On Sat, Jul 25, 2015 at 8:55 PM, Jonathan Alvarsson
> <jonathan.alvarsson@...> wrote:
> > I remember thinking about this years ago and then opting for not adding
> it.
> > Mainly becasue writing the script would be complicated. However, since
> you
> > want it I don't see any reason for why we should not add it. Remind me,
> is
> > there a scripting manager yet? Otherrwise I guess it would belong on the
> UI
> > manager or so...
>
> There is a js manager, but that is linked to the JavaScript console...
> it has stuff like js.say()... in Groovy you can just use "print" so
> that was never a problem to me...
>
> UI sounds appropriate, more than bioclipse, as these messages are
> meant for the UI...
>
> I played with ui.progressMessage(String message, IProgressMonitor
> monitor) ... that the monitor that method gets seems different,
> because I could not get those message to show up in the GroovyConsole
> "monitor"...
>
> Egon
>
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
> ImpactStory: https://impactstory.org/EgonWillighagen
>
--
// Jonathan

On Sat, Jul 25, 2015 at 8:55 PM, Jonathan Alvarsson
<jonathan.alvarsson@...> wrote:
> I remember thinking about this years ago and then opting for not adding it.
> Mainly becasue writing the script would be complicated. However, since you
> want it I don't see any reason for why we should not add it. Remind me, is
> there a scripting manager yet? Otherrwise I guess it would belong on the UI
> manager or so...
There is a js manager, but that is linked to the JavaScript console...
it has stuff like js.say()... in Groovy you can just use "print" so
that was never a problem to me...
UI sounds appropriate, more than bioclipse, as these messages are
meant for the UI...
I played with ui.progressMessage(String message, IProgressMonitor
monitor) ... that the monitor that method gets seems different,
because I could not get those message to show up in the GroovyConsole
"monitor"...
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen

I remember thinking about this years ago and then opting for not adding it.
Mainly becasue writing the script would be complicated. However, since you
want it I don't see any reason for why we should not add it. Remind me, is
there a scripting manager yet? Otherrwise I guess it would belong on the UI
manager or so...
On Sat, Jul 25, 2015 at 3:33 PM, Egon Willighagen <
egon.willighagen@...> wrote:
> Hi all,
>
> I was wondering if it was possible to add messages to the progress
> monitor from the scripting environment? js.say() outputs to the
> console, but it would also be nice if I could add info to the process
> in the progress view... that way, it would be easier to see how far a
> job has progressed, without flooding the scripting console...
>
> Egon
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
> ImpactStory: https://impactstory.org/EgonWillighagen
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Bioclipse-users mailing list
> Bioclipse-users@...
> https://lists.sourceforge.net/lists/listinfo/bioclipse-users
>
--
// Jonathan

Hi Stephen,
This was an old prototype plugin for an early version of Bioclipse that was not ported to v2. I think I remember that it had some basic functionality but that the developer did not finish it.
Cheers,
Ola
On 9 feb 2015, at 20:17, Stephen P. Molnar <s.molnar@...> wrote:
> There s a reference in
> http://www.gromacs.org/Downloads/Related_Software/GUI to '
> Bioclipse: there is a plug-in to bioclipse for gromacs,
> http://wiki.bioclipse.net/index.php?title=Gromacs_plugin';.
>
> However, the ULR points back to the Gromos Website. Is there a
> bioclipse gromos plugin? If so, where is it?
>
> Thanks in advance.
>
> --
> Stephen P. Molnar, Ph.D. Life is a fuzzy set
> Foundation for Chemistry Stochastic and Multivariate
> http://www.FoundationForChemistry.com
> (614)312-7528(c)
> Skype: smolnar1
>
>
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Hi Egon,
For reporting in e.g. Decision Support we use Jasper reports. As I remember it you need to create and design a specific report template (preferably using a report designer such as https://community.jaspersoft.com/project/jaspersoft-studio or http://www.jasperassistant.com/), and then at runtime populate the report with contents programmatically. While it would be possible to populate an existing Jasper report via a manager call, a more general way of creating Jasper reports on the fly would probably be rather difficult.
For simpler reports we generate HTML pages that we open in the internal Web browser in Bioclipse. If there is no manager call to create such a page from HTML it would be very easy to implement, I can also think of several convenience methods that would be useful (e.g. shortcuts for creating HTML snippets and CSS).
Ola
On 27 okt 2014, at 22:11, Egon Willighagen <egon.willighagen@...<mailto:egon.willighagen@...>> wrote:
Hi all,
I have seen some nice reports in the past... I was wondering if those were created using Bioclipse manger calls... That is, is there a manager for creating such reports?
Egon
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Hi Valentin,
I apologize for not replying sooner . For some reason I didn't get your answer by email and I didn't think to look in the list archives until today.
This is what I get when I run the commands you suggested in R:
> installed.packages()['rJava','Version']
Error in installed.packages()["rJava", "Version"] :
subscript out of bounds
> installed.packages()['rj','Version']
Error in installed.packages()["rj", "Version"] : subscript out of bounds
My Windows machine is 64-bit. I don't remember which version of Bioclipse I downloaded - 32 or 64-bit. Does it matter? What do you suggest?
I looked in the Bioclipse documentation and didn't see anything about specific R packages, although I shouldn't be surprised that it needs rJava installed.
Thanks for your help,
Steve
-------------
Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
(517) 264-7657
swathen@...

Hi Steve,
The Bioclipse-R Integration does indeed work with R version 3.1.1.
I suspect your troubles might be related to 32-bit and 64-bit incompatibility. Can you provide some info about your system, Java and Bioclipse - which versions you have, in terms of 32-bit vs 64-bit.
Also, can you check of you have the required R packages installed by running these R commands:
installed.packages()['rj','Version']
installed.packages()['rJava','Version']
Cheers,
Valentin
Valentin Georgiev, PhD
Pharmaceutical Bioinformatics
BMC, Uppsala University
Hello,
I tried to use the Bioclipse R console on my Windows 7 machine and got an error message:
Cannot start the RServi instance.
See http://pele.farmbio.uu.se/bioclipse/help/nav/14_1 or the internal Bioclipse help system!
The latest version of R is 3.1.1, but it looks like the Bioclipse-R integration only works with R v2.15
Are there any plans to update the Bioclipse R support to the current version of R?
I did try installing an earlier version of R and setting the R_HOME field at Bioclipse>Preferences...>R, but the R console still does not work.
Thanks,
Steve
-------------
Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
(517) 264-7657
swathen@...

Hello,
I tried to use the Bioclipse R console on my Windows 7 machine and got an error message:
Cannot start the RServi instance.
See http://pele.farmbio.uu.se/bioclipse/help/nav/14_1 or the internal Bioclipse help system!
The latest version of R is 3.1.1, but it looks like the Bioclipse-R integration only works with R v2.15
Are there any plans to update the Bioclipse R support to the current version of R?
I did try installing an earlier version of R and setting the R_HOME field at Bioclipse>Preferences...>R, but the R console still does not work.
Thanks,
Steve
-------------
Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
(517) 264-7657
swathen@...

Hi all,
Bioclipse is again (indirectly) participating in the Google Summer of
Code. Via the NRNB there are two projects ideas on which students can
apply to work on integrating Cytoscape or PathVisio into Bioclipse.
Please see projects ideas 30 and 31 here:
http://nrnb.org/gsoc/index.html#ideas-tab
Please let me and/or Jonathan know if you are interested!
Greetings,
Jonathan & Egon

Hi Dzul,
Regarding the R-integration you can look at the following:
GNU/Linux users experience this error when they don't have write permissions in /usr/local/lib/R/site-library/, and they haven't set a directory in their home directory for installing R packages. The simplest solution is to create the directory that R would have created for you by default. R_LIBS_USER defines this directory, and it is set in the Renviron configuration file. Find your Renviron file (/etc/R/Renviron on Debian and Ubuntu) and run the following command in your terminal:
grep R_LIBS_USER /etc/R/Renviron
on Ununtu 64 bit the output should be:
R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/2.14'}
#R_LIBS_USER=${R_LIBS_USER-'~/Library/R/2.14/library'}
All you need to do is create the directory path from the uncommented line:
mkdir -p ~/R/x86_64-pc-linux-gnu-library/2.14
and restart Bioclipse.
To install Balloon, go to Install>New Feature... and check Balloon (first in the list)
If you still experience problems, please attach log files when you mail.
Cheers
Valentin
On 18 feb 2014, at 08:30, Mdhafiq Mahat <mdhafiqmahat@...<mailto:mdhafiqmahat@...>> wrote:
Hi there,
I am using ubuntu 12.04, R 3.0.2 and bioclipse 2.6
my problem is there is not acces to the R-console. beside that I cannot convert SDF file to sdf_3D file because there is no balloon..
Dzul
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